Floral ontogeny and anatomy of the hemiparasitic shrub Gaiadendron punctatum and a comparison of floral characters in the tribes Gaiadendrinae and Nuytsiae (Loranthaceae) / Ontogenia floral y anatomía del arbusto hemiparasítico Gaiadendron punctatum y comparación de caracteres florales en las tribus Gaiadendrinae y Nuytsiae (Loranthaceae)

Abstract Introducction: Gaiadendron punctatum is a hemiparasitic species of Loranthaceae (Tribe Gaiadendreae) that is widely distributed in mountainous regions of Central and South America. Embryological and phylogenetic studies in the family indicate a trend towards reduction of the gynoecium and ovules, the morphology of which supports the current circumscription of Tribe Gaiadendreae (Gaiadendron and Atkinsonia). Molecular phylogenetic studies suggest that Nuytsia, Atkinsonia and Gaiadendron diverged successively, forming a grade at the base of the Loranthaceae, but support values are low. Objetive: In the present study, the floral anatomy of Gaiadendron punctatum was investigated in order to provide additional data to permit comparisons among the three basal-most genera in the Loranthaceae and reevaluate their relationships. Methods: Flowers of G. punctatum were collected at different developmental stages and serial sections were prepared and analyzed by light microscopy. Results: Inflorescence development is acropetal; the flowers are bisexual with an inferior ovary surmounted by a calyculus, a ring-shaped structure lacking vascular tissue; the ovary is comprised of seven basal locules, each with an ategmic, tenuinucellate ovule. Above the locules is a mamelon that is fused with the adjacent tissues. The androecium is comprised of seven epipetalous stamens, the anthers with fibrous endothecium dehiscence through a single longitudinal slit, releasing tricolpated pollen. Conclusions: The results of this study show that Gaiadendron and Atkinsonia share versatile, dorsifixed anthers, while Gaiadendron and Nuytsia share the same mode of anther dehiscence. On the other hand, Gaiadendron shares with members of Tribe Elytrantheae an amyliferous mamelon and an unvascularized calyculus. Combined phylogenetic analyses of morphological and molecular data are desirable to determine whether Tribe Gaiadendreae comprises a clade, a grade or if the two genera are more distantly related.

Resumen Introducción: Gaiadendron punctatum es una especie hemiparásita perteneciente a uno de los tres géneros basales de la familia Loranthaceae, siendo los otros dos Nuytsia y Atkinsonia. El género está conformado por dos especies distribuidas en regiones montañosas de Sudamérica y Centroamérica. Tanto los estudios embriológicos, como los filogenéticos, indican una tendencia hacia la reducción del gineceo y de los óvulos en la familia, cuya morfología respalda la circunscripción de la tribu Gaiadendreae (Gaiadendron y Atkinsonia). Estudios filogenéticos moleculares sugieren que Nuytsia, Atkinsonia y Gaiadendron divergieron sucesivamente, formando un grado en la base de la familia Loranthaceae, pero los valores en los que se sustenta son bajos. Objetivo: En el presente trabajo se describe la anatomía floral de la especie Gaiadendron punctatum con el objetivo de complementar la información embriológica, de manera que se pueda comparar directamente la morfología floral y los caracteres embriológicos entre los tres géneros basales de la familia Loranthaceae y reevaluar sus relaciones. Métodos: Las flores de G. punctatum fueron recolectadas en diferentes estados de desarrollo, se realizaron cortes histológicos seriados, se tiñeron con azul de astra y fucsina, y se analizaron mediante microscopía óptica. Resultados: Las inflorescencias mostraron un desarrollo acrópeto, las flores bisexuales presentaron ovario ínfero con presencia de una estructura en forma de anillo, carente de tejidos vasculares llamada calículo; el ovario se compone por siete lóculos basales, cada uno con un óvulo atégmico tenuinucelar. Por encima de los óvulos, el mamelón se fusiona con los tejidos adyacentes. El androceo está conformado por siete estambres epipétalos, las anteras presentan un endotecio fibroso y granos de polen tricolpados. La dehiscencia de las anteras es mediante una sola apertura longitudinal. Conclusiones: Los resultados del presente trabajo demuestran que Gaiadendron y Atkinsonia comparten anteras dorsifijas y versátiles, mientras Gaiadendron y Nuytsia comparten el tipo de dehiscencia anteral y por otro lado Gaiadendron comparte los caracteres de mamelón amilífero y calículo no vascularizado con la tribu Elytrantheae. La clasificación del género Gaiadendron con respecto a los dos géneros basales de la familia debe ser objeto de investigación (análisis filogenético combinado) que permita dirimir si la tribu Gaiadendrae es un clado, un grado o dos géneros más lejanamente emparentados.

Polimorfismos de un solo nucleótido representativos para los alelos clásicos del antígeno leucocitario humano en familias antioqueñas con diabetes mellitus tipo 1 / Classical HLA alleles tag SNP in families from Antioquia with type 1 diabetes mellitus

Resumen Introducción. La región del antígeno leucocitario humano (Human Leukocyte Antigen, HLA) se ha asociado claramente con enfermedades autoinmunitarias, como la diabetes mellitus de tipo 1. Los polimorfismos representativos de un solo nucleótido (tag Single Nucleotide Polymorphism, tag SNP) constituyen una forma alternativa de evaluar los alelos clásicos del HLA. En la población europea se ha reportado un grupo de tag SNP para múltiples alelos clásicos relacionados con la predisposición o la resistencia frente a dicha enfermedad. Objetivo. Validar la metodología basada en los tag SNP enfocada en la inferencia de alelos HLA clásicos, y evaluar su asociación con la diabetes mellitus de tipo 1 en una muestra de familias antioqueñas. Materiales y métodos. Se estudió una muestra de 200 familias antioqueñas con uno a dos hijos afectados por diabetes mellitus de tipo 1. Se genotipificaron 13 SNP mediante el ARMS-PCR (Amplification Refractory Mutation System-Polymerase Chain Reaction) con cuatro iniciadores, o mediante la PCR-RFLP (PCR-Restriction Fragment Length Polymorphism). Además, se evaluó la validez de los tag SNP de 1.000 genomas reportados en europeos en una muestra de 60 individuos de la población colombiana de Medellín. Se hicieron las pruebas de desequilibrio de la transmisión, de desequilibrio de ligamiento y de equilibrio de Hardy-Weinberg. Resultados. En la población de estudio no se encontró suficiente desequilibrio de ligamiento entre los SNP y los alelos clásicos evaluados, por lo cual no fue posible inferir los alelos clásicos del HLA para el conjunto de familias con diabetes mellitus de tipo 1. El estudio de asociación evidenció que esta región aporta factores tanto de riesgo como de protección para el desarrollo de la enfermedad. Los tag SNP apropiados para la muestra de estudio se determinaron usando los SNP ubicados en la región HLA en la base de datos del 1000 Genomes Project en la mencionada población. Conclusiones. Los patrones de desequilibrio de ligamiento en la población estudiada fueron diferentes a los reportados para la población europea. A pesar de esto, se encontró evidencia clara sobre el papel de la región HLA en el riesgo de padecer diabetes mellitus de tipo 1 en la población de estudio.

abstract Introduction: The HLA region strongly associates with autoimmune diseases, such as type 1 diabetes. An alternative way to test classical HLA alleles is by using tag SNP. A set of tag SNP for several classical HLA alleles has been reported as associated with susceptibility or resistance to this disease in Europeans. Objective: We aimed at validating the methodology based on tag SNP focused on the inference of classical HLA alleles, and at evaluating their association with type 1 diabetes mellitus in a sample of 200 families from Antioquia. Materials and methods: We studied a sample of 200 families from Antioquia. Each family had one or two children with T1D. We genotyped 13 SNPs using tetra-primer ARMS-PCR or PCRRFLP. In addition, we tested the validity of the tag SNP reported for Europeans in 60 individuals from a population of Colombians living in Medellín (CLM) from the 1000 Genomes Project database. Statistical analyses included the Hardy-Weinberg equilibrium, the transmission disequilibrium and the linkage disequilibrium tests. Results: The linkage disequilibrium was low in reported tag SNP and classical HLA alleles in this CLM population. Association analyses revealed both risk and protection factors to develop type 1 diabetes mellitus. Appropriate tag SNPs for the CLM population were determined by using the genotype information available in the 1000 Genome Project database. Conclusions: Although linkage disequilibrium patterns in this CLM population were different from those reported in Europeans, we did find strong evidence of the role of HLA in the development of type 1 diabetes mellitus in the study population.

ITPKC and SLC11A1 Gene Polymorphisms and Gene-Gene Interactions in Korean Patients with Kawasaki Disease

PURPOSE: Kawasaki disease (KD) is an acute systemic vasculitis. Both the etiology of KD and the erythema of Bacille Calmette-Guérin (BCG) injection sites observed in the disease are poorly understood. We investigated the association between KD and single nucleotide polymorphisms (SNPs) in two candidate genes: inositol 1,4,5-triphosphate 3-kinase (ITPKC), a well-studied KD-associated gene, and solute carrier 11a1 (SLC11A1), which is associated with the hypersensitive reaction to the BCG strain in Koreans. MATERIALS AND METHODS: Associations between KD and SNPs in two genes were evaluated. Potential associations between BCG injection site erythema and SNPs in two genes were also evaluated. Gene-gene interactions between ITPKC and SLC11A1 in KD and BCG injection site erythema were also analyzed. RESULTS: Three tagging SNPs in ITPKC and five tagging SNPs in SLC11A1 were genotyped in 299 KD patients and 210 control children. SNP rs28493229 in ITPKC was associated with KD and coronary artery complications. SNP rs77624405 in SLC11A1 was associated with KD. Comparisons of KD patients with and without BCG injection site erythema revealed that SNP rs17235409 in SLC11A1 was associated with erythema; no erythema-associated SNPs in ITPKC were identified. Interactions between ITPKC rs28493229_GG and SLC11A1 rs17235409_GA and between ITPKC rs10420685_GG and SLC11A1 rs17235409_AA were strongly associated with BCG injection site erythema. CONCLUSION: This study identified several important polymorphisms in the ITPKC and SLC11A1 genes in Koreans. The genetic variants identified in this study affected KD and erythema of BCG injection sites independently and through gene-gene interactions. Also, the effects of the polymorphisms were age-dependent.

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2... K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high ¨positive¨ (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller ¨negative¨ (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

Epistasis between COMT Val158Met and DRD3 Ser9Gly polymorphisms and cognitive function in schizophrenia: genetic influence on dopamine transmission

Objective:To assess the relationship between cognitive function, a proposed schizophrenia endophenotype, and two genetic polymorphisms related to dopamine function, catechol-O-methyl transferase (COMT) Val158Met and dopamine receptor 3 (DRD3) Ser9Gly.Methods:Fifty-eight outpatients with schizophrenia/schizoaffective disorder and 88 healthy controls underwent neurocognitive testing and genotyping. Analyses of covariance (ANCOVAs) using age, sex, and years of education as covariates compared cognitive performance for the proposed genotypes in patients and controls. ANCOVAs also tested for the epistatic effect of COMT and DRD3 genotype combinations on cognitive performance.Results:For executive functioning, COMT Val/Val patients performed in a similar range as controls (30.70-33.26 vs. 35.53-35.67), but as COMT Met allele frequency increased, executive functioning worsened. COMT Met/Met patients carrying the DRD3 Ser/Ser genotype performed poorest (16.184 vs. 27.388-31.824). Scores of carriers of this COMT/DRD3 combination significantly differed from all DRD3 Gly/Gly combinations (p < 0.05), from COMT Val/Met DRD3 Ser/Gly (p = 0.02), and from COMT Val/Val DRD3 Ser/Ser (p = 0.01) in patients. It also differed significantly from all control scores (p < 0.001).Conclusion:Combined genetic polymorphisms related to dopamine neurotransmission might influence executive function in schizophrenia. Looking at the effects of multiple genes on a single disease trait (epistasis) provides a comprehensive and more reliable way to determine genetic effects on endophenotypes.

Association between peroxisome proliferator-activated receptor and gene-gene interactions with the apolipoprotein A I/apolipoprotein B100 ratio / 中华心血管病杂志

<p><b>OBJECTIVE</b>To investigate the association between ten single nucleotide polymorphisms (SNPs) in the peroxisome proliferator-activated receptors (PPARα, β, γ) with apolipoprotein A I/apolipoprotein B100 (ApoA I/ApoB100) ratio and the additional role of a gene-gene interactions among the 10 SNPs.</p><p><b>METHODS</b>Participants were recruited under the framework of the Prevention of Multiple Metabolic Disorders and Metabolic Syndrome in Jiangsu Province (PMMJS) cohort population survey in the urban community of Jiangsu province of China.A total of 630 subjects were randomly selected and no individual was related.Ten SNPs (rs135539, rs4253778, rs1800206, rs2016520, rs9794, rs10865710, rs1805192, rs709158, rs3856806 and rs4684847) were selected from the HapMap database,which covered PPARα, PPARβ and PPARγ. A linear regression model was used to analyze the relations between ten SNPs in the PPARs and ApoA I/ApoB100 ratio level. Mean difference and 95% CI were calculated. Interactions were explored by using the method of Generalized Multifactor Dimensionality Reduction (GMDR).</p><p><b>RESULTS</b>After adjusting for age, gender, smoking status, alcohol consumption, occupational physical activity, high-fat diet as well as low-fiber diet, both rs1800206 and rs3856806 were significantly associated with a decreased level of ApoA I/ApoB100 ratio, mean difference (95% CI) values were -1.19 (-1.88 to -0.50) and -0.77 (-1.40 to -0.14). Whereas rs4253778 was significantly associated with an increased level of ApoA I/ApoB100 ratio, Mean difference (95% CI) values was 0.80 (0.08 to 1.52). GMDR analysis showed a significant gene-gene interaction among rs4253778, rs1800206 of PPARα, rs9794, rs2016520 of PPARβ and rs10865710, rs3856806, rs709158, rs1805192 of PPARγ for eight-dimension models (P = 0.01), in which prediction accuracy was 0.624 and cross-validation consistency was 7/10.</p><p><b>CONCLUSIONS</b>The rs1800206 of PPARα and rs3856806 of PPARγ are significantly associated with a decreased level of ApoA I/ApoB100 ratio while rs4253778 of PPARα is associated with an increased level of ApoA I/ApoB100 ratio. There is a gene-gene interaction between multiple SNPs.</p>

Associations of Crohn's disease with DR4 and DR5 gene polymorphisms / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To assess the associations of death receptor DR4 and DR5 gene polymorphisms with Crohn's disease (CD).</p><p><b>METHODS</b>A total of 295 CD patients and 490 healthy controls were recruited. Three single nucleotide polymorphisms (SNPs) of the DR4 (rs13278062, rs20575) and DR5 (rs1047266) genes were determined with a SNaPshot method. Unconditional logistic regression analysis was carried out for determining the allelic and genotypic differences of the three SNPs between CD patients and the controls, as well as the influence of the DR4 and DR5 gene polymorphisms on the clinical features of CD patients. Linkage disequilibrium and haplotype analysis were calculated by haplotype 4.2 and R language software. A gene-gene interaction model was established to analyze whether the three SNPs can exert a synergistic effect on the susceptibility to CD.</p><p><b>RESULTS</b>The mutant allele (T) and genotype (GT+TT) of DR4 (rs13278062) were increased among CD patients compared to the controls (37.12% vs. 32.04%, P = 0.040, 95%CI: 1.010-1.550; 62.71% vs. 54.90%, P = 0.032, 95%CI: 1.028-1.855, respectively). However, the allelic and genotypic frequencies of DR4 (rs20575) and DR5 (rs1047266) did not differ between the two groups (all P > 0.05). Based on the Montreal Classification Standards, the CD patients were stratified by locations and behaviors of the disease. After multiple comparison correction (P < 0.0125), compared to ileocolonic CD patients respectively, the mutant allele (T) and genotype (GT+TT) of the rs13278062 polymorphism were significantly increased in colonic CD patients (41.04% vs. 25.64%, P = 0.002, 95%CI: 0.315-0.778; 66.04% vs. 41.03%, P = 0.001, 95%CI: 0.196-0.655, respectively) and terminal ileum CD patients (41.44% vs. 25.64%, P = 0.002, 95%CI: 0.311-0.762; 74.77% vs. 41.03%, P < 0.001, 95%CI: 0.126-0.437, respectively). In comparison to penetrating CD patients, the mutant allele (T) and genotype (GT+TT) of DR4 (rs13278062) were significantly decreased in stricturing CD patients (32.29% vs. 48.91%, P = 0.007, 95%CI: 0.300-0.828; 57.29% vs. 86.96%, P = 0.001, 95%CI: 0.078-0.520, respectively). A similar conclusion was drawn for the mutant genotype (GT+TT) of DR4 (rs13278062) in non-stricturing, non-penetrating CD patients (58.82% vs. 86.96%, P = 0.001, 95%CI: 0.086-0.536). Haplotype analysis indicated that the CT haplotype formed by rs20575 and rs13278062 was increased in CD patients compared to the controls (37.1% vs. 31.8%, P = 0.029, OR=1.279, 95%CI: 1.022-1.600). The outcome of a gene-gene interaction model indicated that the mutant genotype (GT+TT) of DR4 (rs13278062) and mutant genotype (CT+TT) of DR5 (rs1047266) may play a negatively synergistic role in CD patients (B = - 0.483, OR = 0.617, P = 0.030).</p><p><b>CONCLUSION</b>The rs13278062 polymorphism of the DR4 gene not only can confer an increased risk for CD, but may also influence the location of the lesions and the disease behaviors. The CT haplotype formed by rs20575 and rs13278062 may be an independent risk factor for CD. Furthermore, the mutant genotype (GT+TT) of DR4 (rs13278062) and mutant genotype (CT+TT) of DR5 (rs1047266) may exert a negative synergistic effect on CD.</p>

The structure of selective dinucleotide interactions and periodicities in D melanogaster mtDNA

BACKGROUND: We found a strong selective 3-sites periodicity of deviations from randomness of the dinucleotide (DN) distribution, where both bases of DN were separated by 1, 2, K sites in prokaryotes and mtDNA. Three main aspects are studied. I) the specific 3 K-sites periodic structure of the 16 DN. II) to discard the possibility that the periodicity was produced by the highly nonrandom interactive association of contiguous bases, by studying the interaction of non-contiguous bases, the first one chosen each I sites and the second chosen J sites downstream. III) the difference between this selective periodicity of association (distance to randomness) of the four bases with the described fixed periodicities of base sequences. RESULTS: I) The 16 pairs presented a consistent periodicity in the strength of association of both bases of the pairs; the most deviated pairs are those where G and C are involved and the least deviated ones are those where A and T are involved. II) we found significant non-random interactions when the first nucleotide is chosen every I sites and the second J sites downstream until I=J=76. III) we showed conclusive differences between these internucleotide association periodicities and sequence periodicities. CONCLUSIONS: This relational selective periodicity is different from sequence periodicities and indicates that any base strongly interacts with the bases of the residual genome; this interaction and periodicity is highly structured and systematic for every pair of bases. This interaction should be destroyed in few generations by recurrent mutation; it is only compatible with the Synthetic Theory of Evolution and agrees with the Wright's adaptive landscape conception and evolution by shifting balanced adaptive peaks.

Evidencia de asociación entre el gen SLC6A4 y efectos epistáticos con variantes en HTR2A en la etiología del autismo en la población antioqueña / Evidence for association and epistasis between the genetic markers SLC6A4 and HTR2A in autism etiology

Introducción. El espectro autista constituye un grupo de trastornos graves del neurodesarrollo, con un fuerte componente genético. Se ha sugerido un papel importante del sistema serotoninérgico en el desarrollo de este grupo de trastornos, con base en los estudios de respuesta a medicamentos y la hiperserotoninemia, característica común en el autismo. Se han implicado múltiples moléculas en el metabolismo y la neurotransmisión de la serotonina; sin embargo, los resultados de los estudios han tenido poca congruencia entre diferentes poblaciones. Objetivos. Evaluar la relación entre el autismo y el polimorfismo de nucleótido simple (Single Nucleotide Polymorphism, SNP) en los genes SLC6A4, HTR2A e ITGB3, en una muestra de la población antioqueña. Materiales y métodos. Se genotipificaron 42 núcleos familiares con autismo para 10 variantes en los genes SLC6A4, ITGB3 y HTR2A. Se evaluó la asociación utilizando la prueba de desequilibrio en la transmisión. Se exploró el impacto de la interacción entre estos genes y el autismo, utilizando la reducción multidimensional. Resultados. Se encontró asociación de las variantes rs4583306 (OR=2,6, p=0,004) y rs2066713 (OR=2,2 p=0,03), en el gen SLC6A4, y asociación de combinaciones genotípicas entre los genes SLC6A4 y HTR2A y el riesgo de autismo (p=0,0001). Conclusiones. Se encontró asociación significativa con variantes en el gen transportador de serotonina con el autismo, al igual que interacción entre variantes en los genes HTR2A con SLC6A4. Estos resultados concuerdan con los de estudios previos en otras poblaciones y son pruebas a favor del papel del sistema serotoninérgico en la etiología del espectro autista.

Introduction. Autism spectrum disorders are severe neurodevelopmental disorders with a strong genetic component. The potential role of the serotoninergic system in the development of autistic disorder has been based on the observation of hyperserotoninemia in autistic subjects and the results of drug treatment studies. Multiple molecules involved in serotonin metabolism and neurotransmission have been studied; however, replication studies have been inconsistent. This may be partially related to the marked genetic heterogeneity of autism in different populations. Objectives. The relationship between autism and single nucleotide polymorphisms of SLC6A4, HTR2A and ITGB3 genes was evaluated in an urban population of northwestern Colombia. Materials and methods. In Antioquia, Colombia, 42 families with history of autism were screened for 10 SNPs in SLC6A4, HTR2A and ITGB3 genes and evaluated for associations with the transmission disequilibrium test. The interactions among these genes and autism was assessed with multidimensional reduction methods. Results. A significant main effect was seen among the SLC6A4 gene variants rs4583306 (OR=2.6, p=0.004) and rs2066713 (OR=2.2, p=0.03). No main effect of the ITGB3 or HTR2A variants was found, however, in the interaction effects, the SLC6A4 and HTR2A genes demonstrated significant evidence of association with autism (p<0.001). Conclusion. Significant association of markers were discovered within the SLC6A4 gene and the combination of SLC6A4 and HTR2A (S-A) genes to autism. These results were consistent with previous studies conducted in other populations and provide further evidence for the implication of the serotoninergic system in the etiology of autistic disorders.

Epistatic interactions in idiopathic pulmonary arterial hypertension.

BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a poorly understood complex disorder, which results in progressive remodeling of the pulmonary artery that ultimately leads to right ventricular failure. A two-hit hypothesis has been implicated in pathogenesis of IPAH, according to which the vascular abnormalities characteristic of PAH are triggered by the accumulation of genetic and/or environmental insults in an already existing genetic background. The multifactor dimensionality reduction (MDR) analysis is a statistical method used to identify gene–gene interaction or epistasis and gene–environment interactions that are associated with a particular disease. The MDR method collapses high-dimensional genetic data into a single dimension, thus permitting interactions to be detected in relatively small sample sizes. AIM: To identify and characterize polymorphisms/genes that increases the susceptibility to IPAH using MDR analysis. MATERIALS AND METHODS: A total of 77 IPAH patients and 100 controls were genotyped for eight polymorphisms of five genes (5HTT, EDN1, NOS3, ALK-1, and PPAR-γ2). MDR method was adopted to determine gene–gene interactions that increase the risk of IPAH. RESULTS: With MDR method, the single-locus model of 5HTT (L/S) polymorphism and the combination of 5HTT(L/S), EDN1(K198N), and NOS3(G894T) polymorphisms in the three-locus model were attributed to be the best models for predicting susceptibility to IPAH, with a P value of 0.05. CONCLUSION: MDR method can be useful in understanding the role of epistatic and gene–environmental interactions in pathogenesis of IPAH.

Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

Epistasis (gene-gene interaction) is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G) and RETN (SNP-420C > G and SNP+299G > A) gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM) and metabolic syndrome (MS) were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles) of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles) of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

Inclusão da epistasia em modelo de avaliação genética de bovinos de corte compostos / The effect of the inclusion of epistasis on the genetic evaluation model of beef cattle composite

Dados de bovinos compostos foram analisados para avaliar o efeito da epistasia nos modelos de avaliação genética. As características analisadas foram os pesos aos 205 (P205) e 390 dias (P390) e perímetro escrotal aos 390 dias (PE390). As análises foram realizadas pela metodologia de máxima verossimilhança considerando-se dois modelos: o modelo 1 incluiu como covariáveis os efeitos aditivos diretos e maternos, e os não aditivos das heterozigoses para os efeitos diretos e para o materno total, e o modelo 2 considerou também o efeito direto de epistasia. Para comparação dos modelos, foram utilizados o critério de informação de Akaike (AIC) e o critério de informação Bayesiano de Schwartz (BIC), e o teste de razão de verossimilhança. A inclusão da epistasia no modelo de avaliação genética pouco alterou as estimativas de componentes de (co)variâncias genéticas aditivas e, consequentemente, as herdabilidades. O teste de verossimilhança e o critério de Akaike sugeriram que o modelo 2, que inclui a epistasia, apresentou maior aderência aos dados para todas as características analisadas. O critério BIC indicou este modelo como o melhor apenas para P205. Para análise genética dessa população, o modelo que considerou o efeito de epistasia foi o mais adequado.

Composite bovine data was analyzed with the objective of evaluating the effect of the epistasis parameter in the models of genetic evaluation. The analyzed characteristics were weight at 205 (W205) and 390 days (P390), and scrotal circumference at 390 days (SC390). The analysis were done by the maximum likelihood method, considering two models: model 1, which included as covariates the direct and maternal additive effects, and non-additive of the heterozygosis for the direct and total maternal, and model 2, which also considered the direct epistasis direct. The Akaike Information Criteria (AIC) and the Bayesiano of Schwartz Information Criteria (BIC) were used for the comparison of the models and the test of ratio of likelihood. The inclusion of the epistasis effects on the model of the genetic evaluation did not alter much the estimation of the genetic additive (co)variances components and, consequently the heritability. However, it was significantly superior by the likelihood ratio test for the studied characteristics. Through the BIC, model 2 was more adequate only for W205. For the genetic analysis of that population the model that considers the epitasis is the more adequate.

Complex genetic mechanisms in glaucoma: An overview.

Glaucomas comprise a group of hereditary optic neuropathies characterized by progressive and irreversible visual field loss and damage to the optic nerve head. It is a complex disease with multiple molecular mechanisms underlying its pathogenesis. Genetic heterogeneity is the hallmark of all glaucomas and multiple chromosomal loci have been linked to the disease, but only a few genes have been characterized, viz. myocilin (MYOC), optineurin (OPTN), WDR36 and neurotrophin-4 (NTF4) in primary open angle glaucoma (POAG) and CYP1B1 and LTBP2 in congenital and developmental glaucomas. Case-control-based association studies on candidate genes involved in different stages of glaucoma pathophysiology have indicated a very limited involvement. The complex mechanisms leading to glaucoma pathogenesis indicate that it could be attributed to multiple genes with varying magnitudes of effect. In this review, we provide an appraisal of the various efforts in unraveling the molecular mystery in glaucoma and also some future directions based on the available scientific knowledge and technological developments.

Mechanism and methods to induce pluripotency

Pluripotent stem cells are able to self-renew indefinitely and differentiate into all types of cells in the body. They can thus be an inexhaustible source for future cell transplantation therapy to treat degenerative diseases which currently have no cure. However, non-autologous cells will cause immune rejection. Induced pluripotent stem cell (iPSC) technology can convert somatic cells to the pluripotent state, and therefore offers a solution to this problem. Since the first generation of iPSCs, there has been an explosion of relevant research, from which we have learned much about the genetic networks and epigenetic landscape of pluripotency, as well as how to manipulate genes, epigenetics, and microRNAs to obtain iPSCs. In this review, we focus on the mechanism of cellular reprogramming and current methods to induce pluripotency. We also highlight new problems emerging from iPSCs. Better understanding of the fundamental mechanisms underlying pluripotenty and refining the methodology of iPSC generation will have a significant impact on future development of regenerative medicine.

Cytogenetic analysis of five Hypostomus species (Siluriformes, Loricariidae)

In this work, we analyzed the karyotypes of five species. Hypostomus cf. heraldoi, from the Mogi-Guaçu River, had 2n = 72 chromosomes, with a nucleolar organizer region (NOR) in one chromosomal pair. Hypostomus regani, from the Mogi-Guaçu River had 2n = 72 chromosomes with NORs in two chromosomal pairs. Hypostomus sp., from the Mogi-Guaçu River basin, had 2n = 68 chromosomes, with NORs in two chromosomal pairs. Hypostomus aff. agna, from Cavalo Stream, had 2n = 74 chromosomes with NORs in two chromosomal pairs. Hypostomus cf. topavae, from Carrapato Stream, had 2n = 80 chromosomes, with NORs in two chromosomal pairs. Hypostomus species showed marked diversity in the karyotypic formula, which suggested the occurrence of several Robertsonian rearrangements and pericentric inversions during the evolutionary history of this genus. This hypothesis was supported by the occurrence of a large number of uniarmed chromosomes and multiple NORs in a terminal position in most species and may be a derived condition in the Loricariidae.

Avaliação do desempenho na pós-desmama para uma população bovina multirracial Aberdeen Angus x Nelore utilizando-se diferentes modelos genéticos / Post weaning performance evaluation for a multibreed Aberdeen Angus x Nellore population using different genetic models

Com o objetivo de testar modelos genéticos alternativos ao aditivo-dominante em populações multirraciais, foram utilizadas informações do peso ao sobreano (PS) de 35.931 novilhos, filhos de 752 touros e 30.535 vacas das raças Aberdeen Angus (A) e Nelore (N) e de diversos grupos genéticos possíveis por meio do cruzamento entre elas. Foram testados cinco diferentes modelos (M) genéticos: o M1 continha o efeito genético fixo aditivo direto (AD), heterozigótico direto (HD), epistático direto (ED) e aditivo-conjunto direto (ACD); o M2, igual ao M1, menos o efeito ACD; o M3, igual ao M1, menos o efeito ED; o M4, igual ao M1, menos os efeitos ED e ACD; e o M5, igual ao M1, menos os efeitos HD, ED e ACD. Os modelos foram submetidos a três métodos de análise diferentes: método dos quadrados mínimos (MQM), regressão de cumeeira (RC) e máxima verossimilhança restrita (REML). O método de RC produziu estimativas de coeficientes com magnitudes e sinais explicados biologicamente. As estimativas dos efeitos, das (co)variâncias, dos parâmetros e dos valores genéticos diferiram entre os modelos, indicando a importância da correta escolha do modelo de análise, devendo-se ter conhecimento prévio do fenômeno estudado e sua interpretação biológica e sempre preceder à escolha de um modelo de análise genética multirracial o estudo da relação existente entre as variáveis independentes. Importantes efeitos adicionais ao efeito AD foram acrescentados pelas inclusões dos efeitos HD e ED aos modelos de análise. A notação matemática dos efeitos ACD, aplicada atualmente na literatura e testada neste estudo, não foi capaz de explicar a complementaridade entre raças como esperado, havendo problemas com casos de multicolinearidade entre os efeitos estudados.

In order to evaluate alternative genetic models to the additive dominant model, weights at yearling (PS) of 35,931 animals, sired by 752 bulls and 30,535 cows of Aberdeen Angus (A) and Nellore (N) breeds and the genetic groups from their crosses were used. Five different genetic models (M) were tested: M1, containing the direct additive fixed genetic effect (DA), heterozygote direct (HD), epystatic direct (ED), and direct joint additive direct (DJA); M2 was equal to M1, excluding DJA effect; M3 was equal to M1, excluding ED effect; M4 was equal M1, excluding ED and ACD effects, and M5 was equal to M1, excluding HD, ED, and DJA effects. The models were analyzed by different methods: Least Square Means Method (MQM), Ridge Regression Method (RC), and Restricted Maximum Likelihood Method (REML). Estimated coefficients by RC showed magnitude and sign which were biologically explained. The estimates of the covariances, parameters, and genetic values varied among the models, indicating the importance of the correct choice of the model for analysis, being necessary a previous knowledge of the studied phenomenon and its biological interpretation. Besides, it should always be considered the relationship between the independent variables before choosing a multibreed genetic analysis model. Important additional effects to the DA effect were considered by the inclusion of the HD and ED effects to the models for analysis. The DJA math notation, currently used in the literature and tested in the present study, was not able to explain the breed complementarity, due to the multi colinearity among the studied effects.

Identification of gene-gene interactions related to the etiology of complex disease: a multifactor dimensionality reduction-genotype pedigree disequilibrium test / 中华流行病学杂志

<p><b>UNLABELLED</b>To introduce the application of a multifactor dimensionality reduction-genotype pedigree disequilibrium test (MDR-PDT) for detecting gene-gene interactions in the etiology of complex disease. A brief overview on the basic theory, implementing steps and features of MDR-PDT were described, and a practical research case was demonstrated to application of MDR-PDT in nuclear family studies. The MDR-PDT approach was the extension or development of conventional MDR method which could be used for detecting gene-gene interactions in families of diverse structure.</p><p><b>CONCLUSION</b>MDR-PDT was a new nonparametric and model-free method which might use additional family members in the nuclear families and had a good power to identify gene-gene interactions.</p>